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Tav4SB: integrating tools for analysis of kinetic models of biological systems

Mikołaj Rybiński12*, Michał Lula1, Paweł Banasik1, Sławomir Lasota1 and Anna Gambin12

Author affiliations

1 Institute of Informatics, University of Warsaw, ul. Banacha 2, 02-097, Warsaw, Poland

2 Mossakowski Medical Research Centre, Polish Academy of Sciences, ul. Pawińskiego 5, 02-106, Warsaw, Poland

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Citation and License

BMC Systems Biology 2012, 6:25  doi:10.1186/1752-0509-6-25

Published: 5 April 2012

Abstract

Background

Progress in the modeling of biological systems strongly relies on the availability of specialized computer-aided tools. To that end, the Taverna Workbench eases integration of software tools for life science research and provides a common workflow-based framework for computational experiments in Biology.

Results

The Taverna services for Systems Biology (Tav4SB) project provides a set of new Web service operations, which extend the functionality of the Taverna Workbench in a domain of systems biology. Tav4SB operations allow you to perform numerical simulations or model checking of, respectively, deterministic or stochastic semantics of biological models. On top of this functionality, Tav4SB enables the construction of high-level experiments. As an illustration of possibilities offered by our project we apply the multi-parameter sensitivity analysis. To visualize the results of model analysis a flexible plotting operation is provided as well. Tav4SB operations are executed in a simple grid environment, integrating heterogeneous software such as Mathematica, PRISM and SBML ODE Solver. The user guide, contact information, full documentation of available Web service operations, workflows and other additional resources can be found at the Tav4SB project’s Web page: http://bioputer.mimuw.edu.pl/tav4sb/ webcite.

Conclusions

The Tav4SB Web service provides a set of integrated tools in the domain for which Web-based applications are still not as widely available as for other areas of computational biology. Moreover, we extend the dedicated hardware base for computationally expensive task of simulating cellular models. Finally, we promote the standardization of models and experiments as well as accessibility and usability of remote services.